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Phenotypic consequences of heterozygosity Homozygosity for deletion is often but not always lethal Homozygosity for deletion is often but not always lethal Heterozygosity for deletion is often detrimental Heterozygosity for deletion is often detrimental Fig. 13.3

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Deletion heterozygotes affect mapping distances Recombination between homologues can only occur if both carry copies of the gene Recombination between homologues can only occur if both carry copies of the gene Deletion loop formed if heterozygous for deletion Deletion loop formed if heterozygous for deletion Identification of deletion location on chromosome Identification of deletion location on chromosome Genes within can not be separated by recombination Genes within can not be separated by recombination Fig a

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Deletions to locate genes at the molecular level Labeled probe hybridizes to wild-type chromosome but not to deletion chromosome Labeled probe hybridizes to wild-type chromosome but not to deletion chromosome Fig a

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Duplication loops form when chromosomes pair in duplication heterozygotes In prophase I, the duplication loop can assume different configurations that maximize the pairing of related regions In prophase I, the duplication loop can assume different configurations that maximize the pairing of related regions Fig c

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Unequal crossing over between duplications increases or decreases gene copy number Fig

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Summary of duplication and deletion effects on phenotpye Alter number of genes on a chromosome and may affect phenotype of heterozygote Alter number of genes on a chromosome and may affect phenotype of heterozygote Heterozygosity create one or three gene copies and create imbalance in gene product altering phenotypes (some lethal) Heterozygosity create one or three gene copies and create imbalance in gene product altering phenotypes (some lethal) Genes may be placed in new location that modifies its expression Genes may be placed in new location that modifies its expression Deletions and duplications drive evolution by generating families of tandemly repeated genes Deletions and duplications drive evolution by generating families of tandemly repeated genes

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Inversions reorganize the DNA sequence of a chromosome Produced by half rotation of chromosomal regions after double-stranded break Produced by half rotation of chromosomal regions after double-stranded break Also rare crossover between related genes in opposite orientation or transposition Also rare crossover between related genes in opposite orientation or transposition Fig a,b

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Translocations attach on part of a chromosome to another Translocation – part of one chromosome becomes attached to nonhomologous chromosome Translocation – part of one chromosome becomes attached to nonhomologous chromosome Reciprocal translocation – two different parts of chromosomes switch places Reciprocal translocation – two different parts of chromosomes switch places Fig a

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Robertsonian translocations can reshape genomes Reciprocal exchange between acrocentric chromosomes generate large metacentric chromosome and small chromosome Reciprocal exchange between acrocentric chromosomes generate large metacentric chromosome and small chromosome Tiny chromosome may be lost from organism Tiny chromosome may be lost from organism Fig

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Translocation Down syndrome translocation of chromosome 21 is small and thus produces viable gamete, but with phenotypic consequence Fig

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Transposable elements move from place to place in the genome 1930s Marcus Rhoades and 1950s Barbara McClintock – transposable elements in corn 1930s Marcus Rhoades and 1950s Barbara McClintock – transposable elements in corn 1983 McClintock received Nobel Prize 1983 McClintock received Nobel Prize Found in all organisms Found in all organisms Any segment of DNA that evolves ability to move from one place to another in genome Any segment of DNA that evolves ability to move from one place to another in genome Selfish DNA carrying only information to self-perpetuate Selfish DNA carrying only information to self-perpetuate Most 50 – 10,000 bp Most 50 – 10,000 bp May be present hundreds of time in a genome May be present hundreds of time in a genome LINES, long interspersed element in mammals LINES, long interspersed element in mammals ~ 20,000 copies in human genome up to 6.4kb in length ~ 20,000 copies in human genome up to 6.4kb in length SINES, short interspersed elements in mammals SINES, short interspersed elements in mammals ~ 300,000 copies in human genome ~ 300,000 copies in human genome ~ 7% of genome are LINES and SINES ~ 7% of genome are LINES and SINES

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Retroposons generate an RNA that encodes a reverse transciptase like enzyme Two types Two types Poly-A tail at 3’ end of RNA-like DNA strand Poly-A tail at 3’ end of RNA-like DNA strand Long terminal repeat (LTRs) oriented in same direction on either end of element Long terminal repeat (LTRs) oriented in same direction on either end of element Fig a

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P elements in Drosophila After excision of P element transposon, DNA exonucleases first widen gap and then repair it After excision of P element transposon, DNA exonucleases first widen gap and then repair it Repair uses sister chromatid or homologous chromosome as a template Repair uses sister chromatid or homologous chromosome as a template P strains of Drosophila have many copies of P elements P strains of Drosophila have many copies of P elements M strains have no copies M strains have no copies Hybrid dysgenesis – defects including sterility, mutation, and chromosomal breakage from cross between P and M strains Hybrid dysgenesis – defects including sterility, mutation, and chromosomal breakage from cross between P and M strains Promotes movement of P elements to new positions Promotes movement of P elements to new positions

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Genomes often contain defective copies of transposable elements Many TEs sustain deletions during transposition or repair Many TEs sustain deletions during transposition or repair If promoter needed for transcription deleted, TE can not transpose again If promoter needed for transcription deleted, TE can not transpose again Most SINES and LINES in human genome are defective TEs Most SINES and LINES in human genome are defective TEs Nonautonomous elements – need activity of nondeleted copies of same TE for movement Nonautonomous elements – need activity of nondeleted copies of same TE for movement Autonomous elements – move by themselves Autonomous elements – move by themselves

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Triploids are almost always sterile Triploids are almost always sterile Result from union of monoploid and diploid gametes Result from union of monoploid and diploid gametes Meiosis produces unbalanced gametes Meiosis produces unbalanced gametes Fig

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Tetraploids are often source of new species Tetraploids are often source of new species Failure of chromosomes to separate into two daughter cells during mitosis in diploid Failure of chromosomes to separate into two daughter cells during mitosis in diploid Cross between tetraploid and diploid creates triploids – new species, autopolyploids Cross between tetraploid and diploid creates triploids – new species, autopolyploids a

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Maintenance of tetraploid species depends on the production of gametes with balanced sets of chromosomes Maintenance of tetraploid species depends on the production of gametes with balanced sets of chromosomes Bivalents- pairs of synapsed homologous chromosomes that ensure balanced gametes Bivalents- pairs of synapsed homologous chromosomes that ensure balanced gametes Fig b